rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

The following methods produce descriptors of trait distribution among leaf nodes within the trees. They require that a trait has been set for each leaf node. The tag methods of Bio::Tree::Node are used to store them as key/value pairs. In this way, one tree can store more than one trait.

This is the first half of the Fitch algorithm that is enough for calculating the resolved parsimony values. The trait/chararacter states are commonly left in ambiguous state. To resolve them, run fitch_down.

This is a more generic name for ps and indicates that it performs the first bottom-up tree traversal that calculates the parsimony score but usually leaves trait/character states ambiguous. If you are interested in internal trait states, running fitch_down should resolve most of the ambiguities.

Example : persistence($tree, $node);
Description: Calculates the persistence
for node in the subtree defined by the (internal)
node. Node defaults to the root.
Returns : int, number of generations trait value has to remain same
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional

Persistence measures the stability that the trait value has in a tree. It expresses the number of generations the trait value remains the same. All the decendants of the root in the same generation have to share the same value.

Example : count_clusters($tree, $node);
Description: Calculates the number of sub-clusters
in the subtree defined by the (internal)
node. Node defaults to the root.
Returns : int, count
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional

Example : count_leaves($tree, $node);
Description: Calculates the number of leaves with same trait
value as root in the subtree defined by the (internal)
node. Requires an unbroken line of identical trait values.
Node defaults to the root.
Returns : int, number of leaves with this trait value
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional

Example : sum_of_leaf_distances($tree, $node);
Description: Sums up the branch lengths from root to leaf
exluding the subclusters where the trait values
are different
Returns : float, length
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional

Example : genetic_diversity($tree, $node);
Description: Diversity is the sum of root to leaf distances
within the phylotype normalised by number of leaf
nodes
Returns : float, value of genetic diversity
Exceptions : all the nodes need to have the trait defined
Args : 1. Bio::Tree::TreeI object
2. Bio::Tree::NodeI object within the tree, optional